NSD1 mutations generate a genome-wide DNA methylation signature

S. Choufani, C. Cytrynbaum, B. H. Y. Chung, A. L. Turinsky, D. Grafodatskaya, Y. A. Chen, A. S. A. Cohen, L. Dupuis, D. T. Butcher, M. T. Siu, H. M. Luk, I. F. M. Lo, S. T. S. Lam, O. Caluseriu, D. J. Stavropoulos, W. Reardon, R. Mendoza-Londono, M. Brudno, W. T. Gibson, D. Chitayat and R. Weksberg ()
Additional contact information
S. Choufani: Program in Genetics and Genome Biology, The Hospital for Sick Children
C. Cytrynbaum: Program in Genetics and Genome Biology, The Hospital for Sick Children
B. H. Y. Chung: Li Ka Shing Faculty of Medicine, University of Hong Kong
A. L. Turinsky: Program in Genetics and Genome Biology, The Hospital for Sick Children
D. Grafodatskaya: Program in Genetics and Genome Biology, The Hospital for Sick Children
Y. A. Chen: Program in Genetics and Genome Biology, The Hospital for Sick Children
A. S. A. Cohen: UBC, Child and Family Research Institute
L. Dupuis: The Hospital for Sick Children
D. T. Butcher: Program in Genetics and Genome Biology, The Hospital for Sick Children
M. T. Siu: Program in Genetics and Genome Biology, The Hospital for Sick Children
H. M. Luk: Clinical Genetics Service, Cheung Sha Wan Jockey Club Clinic
I. F. M. Lo: Clinical Genetics Service, Cheung Sha Wan Jockey Club Clinic
S. T. S. Lam: Clinical Genetics Service, Cheung Sha Wan Jockey Club Clinic
O. Caluseriu: University of Alberta
D. J. Stavropoulos: Pediatric Laboratory Medicine, The Hospital for Sick Children
W. Reardon: Our Lady’s Hospital for Sick Children
R. Mendoza-Londono: Program in Genetics and Genome Biology, The Hospital for Sick Children
M. Brudno: Program in Genetics and Genome Biology, The Hospital for Sick Children
W. T. Gibson: UBC, Child and Family Research Institute
D. Chitayat: The Hospital for Sick Children
R. Weksberg: Program in Genetics and Genome Biology, The Hospital for Sick Children

Nature Communications, 2015, vol. 6, issue 1, 1-7

Abstract: Abstract Sotos syndrome (SS) represents an important human model system for the study of epigenetic regulation; it is an overgrowth/intellectual disability syndrome caused by mutations in a histone methyltransferase, NSD1. As layered epigenetic modifications are often interdependent, we propose that pathogenic NSD1 mutations have a genome-wide impact on the most stable epigenetic mark, DNA methylation (DNAm). By interrogating DNAm in SS patients, we identify a genome-wide, highly significant NSD1+/−-specific signature that differentiates pathogenic NSD1 mutations from controls, benign NSD1 variants and the clinically overlapping Weaver syndrome. Validation studies of independent cohorts of SS and controls assigned 100% of these samples correctly. This highly specific and sensitive NSD1+/− signature encompasses genes that function in cellular morphogenesis and neuronal differentiation, reflecting cardinal features of the SS phenotype. The identification of SS-specific genome-wide DNAm alterations will facilitate both the elucidation of the molecular pathophysiology of SS and the development of improved diagnostic testing.

Date: 2015
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DOI: 10.1038/ncomms10207

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